Starting phenix.real_space_refine on Fri Aug 2 19:21:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy0_37914/08_2024/8wy0_37914.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy0_37914/08_2024/8wy0_37914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy0_37914/08_2024/8wy0_37914.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy0_37914/08_2024/8wy0_37914.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy0_37914/08_2024/8wy0_37914.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy0_37914/08_2024/8wy0_37914.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 3021 2.51 5 N 738 2.21 5 O 860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "d GLU 27": "OE1" <-> "OE2" Residue "e GLU 91": "OE1" <-> "OE2" Residue "e GLU 124": "OE1" <-> "OE2" Residue "f GLU 120": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 4656 Number of models: 1 Model: "" Number of chains: 9 Chain: "a" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 234 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "b" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 243 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "d" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 817 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "e" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 959 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "f" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 933 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain breaks: 1 Chain: "g" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 890 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain: "m" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 250 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "n" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 302 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.33, per 1000 atoms: 0.72 Number of scatterers: 4656 At special positions: 0 Unit cell: (70.0245, 90.4932, 106.653, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 860 8.00 N 738 7.00 C 3021 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS a 32 " - pdb=" SG CYS b 32 " distance=2.18 Simple disulfide: pdb=" SG CYS d 37 " - pdb=" SG CYS d 73 " distance=2.03 Simple disulfide: pdb=" SG CYS d 93 " - pdb=" SG CYS d 96 " distance=2.03 Simple disulfide: pdb=" SG CYS e 49 " - pdb=" SG CYS e 98 " distance=2.03 Simple disulfide: pdb=" SG CYS e 119 " - pdb=" SG CYS e 122 " distance=2.03 Simple disulfide: pdb=" SG CYS f 49 " - pdb=" SG CYS f 98 " distance=2.03 Simple disulfide: pdb=" SG CYS f 119 " - pdb=" SG CYS f 122 " distance=2.03 Simple disulfide: pdb=" SG CYS g 46 " - pdb=" SG CYS g 87 " distance=2.03 Simple disulfide: pdb=" SG CYS g 104 " - pdb=" SG CYS g 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 870.7 milliseconds 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1094 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 9 sheets defined 39.7% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'a' and resid 27 through 52 removed outlier: 3.961A pdb=" N TYR a 33 " --> pdb=" O PRO a 29 " (cutoff:3.500A) Processing helix chain 'b' and resid 30 through 56 Processing helix chain 'd' and resid 102 through 126 removed outlier: 3.620A pdb=" N GLY d 106 " --> pdb=" O ALA d 102 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE d 108 " --> pdb=" O VAL d 104 " (cutoff:3.500A) Processing helix chain 'e' and resid 127 through 152 removed outlier: 3.754A pdb=" N THR e 132 " --> pdb=" O MET e 128 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ILE e 133 " --> pdb=" O SER e 129 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER e 152 " --> pdb=" O VAL e 148 " (cutoff:3.500A) Processing helix chain 'f' and resid 104 through 108 removed outlier: 3.773A pdb=" N ASP f 107 " --> pdb=" O LYS f 104 " (cutoff:3.500A) Processing helix chain 'f' and resid 126 through 154 removed outlier: 3.552A pdb=" N VAL f 130 " --> pdb=" O ASP f 126 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU f 147 " --> pdb=" O GLY f 143 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL f 148 " --> pdb=" O LEU f 144 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS f 153 " --> pdb=" O TYR f 149 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN f 154 " --> pdb=" O TYR f 150 " (cutoff:3.500A) Processing helix chain 'g' and resid 76 through 80 removed outlier: 3.513A pdb=" N LYS g 79 " --> pdb=" O SER g 76 " (cutoff:3.500A) Processing helix chain 'g' and resid 114 through 135 Processing helix chain 'm' and resid 260 through 291 removed outlier: 3.528A pdb=" N LEU m 266 " --> pdb=" O ASN m 262 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU m 269 " --> pdb=" O SER m 265 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA m 280 " --> pdb=" O ALA m 276 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA m 291 " --> pdb=" O ALA m 287 " (cutoff:3.500A) Processing helix chain 'n' and resid 272 through 307 removed outlier: 3.927A pdb=" N TYR n 283 " --> pdb=" O THR n 279 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET n 284 " --> pdb=" O SER n 280 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'd' and resid 26 through 28 removed outlier: 7.349A pdb=" N VAL d 33 " --> pdb=" O LEU d 60 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU d 60 " --> pdb=" O VAL d 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'd' and resid 42 through 46 removed outlier: 6.817A pdb=" N ILE d 70 " --> pdb=" O VAL d 44 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR d 71 " --> pdb=" O VAL d 86 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL d 86 " --> pdb=" O TYR d 71 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N THR d 85 " --> pdb=" O TYR e 111 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N TYR e 113 " --> pdb=" O THR d 85 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLN d 87 " --> pdb=" O TYR e 113 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ARG e 115 " --> pdb=" O GLN d 87 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N HIS d 89 " --> pdb=" O ARG e 115 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE e 110 " --> pdb=" O CYS e 98 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N CYS e 98 " --> pdb=" O PHE e 110 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL e 97 " --> pdb=" O GLN e 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'd' and resid 96 through 97 Processing sheet with id=AA4, first strand: chain 'e' and resid 37 through 41 removed outlier: 3.506A pdb=" N LYS e 37 " --> pdb=" O THR e 48 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR e 44 " --> pdb=" O SER e 41 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'f' and resid 37 through 41 removed outlier: 3.985A pdb=" N LYS f 37 " --> pdb=" O THR f 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'f' and resid 113 through 114 removed outlier: 5.541A pdb=" N TYR f 113 " --> pdb=" O TYR g 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'f' and resid 122 through 124 removed outlier: 3.632A pdb=" N ILE g 108 " --> pdb=" O MET f 123 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'g' and resid 31 through 33 removed outlier: 3.910A pdb=" N GLY g 75 " --> pdb=" O VAL g 42 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU g 44 " --> pdb=" O ASN g 73 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ASN g 73 " --> pdb=" O LEU g 44 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'g' and resid 55 through 57 removed outlier: 3.705A pdb=" N GLN g 86 " --> pdb=" O PHE g 56 " (cutoff:3.500A) 214 hydrogen bonds defined for protein. 615 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.15 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1440 1.34 - 1.46: 1109 1.46 - 1.59: 2143 1.59 - 1.71: 0 1.71 - 1.83: 51 Bond restraints: 4743 Sorted by residual: bond pdb=" CA THR f 34 " pdb=" CB THR f 34 " ideal model delta sigma weight residual 1.528 1.553 -0.025 1.68e-02 3.54e+03 2.19e+00 bond pdb=" CA LEU g 110 " pdb=" CB LEU g 110 " ideal model delta sigma weight residual 1.528 1.564 -0.035 2.61e-02 1.47e+03 1.83e+00 bond pdb=" CA ASN e 121 " pdb=" CB ASN e 121 " ideal model delta sigma weight residual 1.533 1.548 -0.015 1.37e-02 5.33e+03 1.18e+00 bond pdb=" C3 CLR b 201 " pdb=" O1 CLR b 201 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.07e+00 bond pdb=" CB ASN d 36 " pdb=" CG ASN d 36 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 1.04e+00 ... (remaining 4738 not shown) Histogram of bond angle deviations from ideal: 100.74 - 107.39: 132 107.39 - 114.04: 2712 114.04 - 120.69: 1900 120.69 - 127.35: 1655 127.35 - 134.00: 31 Bond angle restraints: 6430 Sorted by residual: angle pdb=" CA LYS d 80 " pdb=" CB LYS d 80 " pdb=" CG LYS d 80 " ideal model delta sigma weight residual 114.10 120.87 -6.77 2.00e+00 2.50e-01 1.15e+01 angle pdb=" CA TYR d 79 " pdb=" CB TYR d 79 " pdb=" CG TYR d 79 " ideal model delta sigma weight residual 113.90 119.74 -5.84 1.80e+00 3.09e-01 1.05e+01 angle pdb=" N PRO g 96 " pdb=" CA PRO g 96 " pdb=" C PRO g 96 " ideal model delta sigma weight residual 110.40 115.33 -4.93 1.61e+00 3.86e-01 9.38e+00 angle pdb=" CB LYS f 85 " pdb=" CG LYS f 85 " pdb=" CD LYS f 85 " ideal model delta sigma weight residual 111.30 118.18 -6.88 2.30e+00 1.89e-01 8.96e+00 angle pdb=" CB MET g 103 " pdb=" CG MET g 103 " pdb=" SD MET g 103 " ideal model delta sigma weight residual 112.70 120.71 -8.01 3.00e+00 1.11e-01 7.12e+00 ... (remaining 6425 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 2413 17.75 - 35.50: 374 35.50 - 53.25: 95 53.25 - 70.99: 10 70.99 - 88.74: 5 Dihedral angle restraints: 2897 sinusoidal: 1190 harmonic: 1707 Sorted by residual: dihedral pdb=" CB CYS e 119 " pdb=" SG CYS e 119 " pdb=" SG CYS e 122 " pdb=" CB CYS e 122 " ideal model delta sinusoidal sigma weight residual 93.00 145.92 -52.92 1 1.00e+01 1.00e-02 3.81e+01 dihedral pdb=" CA ASN g 106 " pdb=" C ASN g 106 " pdb=" N CYS g 107 " pdb=" CA CYS g 107 " ideal model delta harmonic sigma weight residual -180.00 -152.37 -27.63 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CB CYS d 37 " pdb=" SG CYS d 37 " pdb=" SG CYS d 73 " pdb=" CB CYS d 73 " ideal model delta sinusoidal sigma weight residual 93.00 53.21 39.79 1 1.00e+01 1.00e-02 2.22e+01 ... (remaining 2894 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 603 0.047 - 0.095: 123 0.095 - 0.142: 32 0.142 - 0.189: 0 0.189 - 0.237: 1 Chirality restraints: 759 Sorted by residual: chirality pdb=" CB ILE f 133 " pdb=" CA ILE f 133 " pdb=" CG1 ILE f 133 " pdb=" CG2 ILE f 133 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA GLU f 91 " pdb=" N GLU f 91 " pdb=" C GLU f 91 " pdb=" CB GLU f 91 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.31e-01 chirality pdb=" CA ILE d 24 " pdb=" N ILE d 24 " pdb=" C ILE d 24 " pdb=" CB ILE d 24 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.13e-01 ... (remaining 756 not shown) Planarity restraints: 786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN e 121 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.18e+00 pdb=" C ASN e 121 " 0.046 2.00e-02 2.50e+03 pdb=" O ASN e 121 " -0.018 2.00e-02 2.50e+03 pdb=" N CYS e 122 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU g 97 " -0.008 2.00e-02 2.50e+03 1.58e-02 2.50e+00 pdb=" C LEU g 97 " 0.027 2.00e-02 2.50e+03 pdb=" O LEU g 97 " -0.010 2.00e-02 2.50e+03 pdb=" N GLN g 98 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS g 95 " -0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO g 96 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO g 96 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO g 96 " -0.021 5.00e-02 4.00e+02 ... (remaining 783 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 152 2.69 - 3.25: 4671 3.25 - 3.80: 7081 3.80 - 4.35: 8584 4.35 - 4.90: 14176 Nonbonded interactions: 34664 Sorted by model distance: nonbonded pdb=" O ILE d 24 " pdb=" OH TYR e 95 " model vdw 2.142 3.040 nonbonded pdb=" OG SER f 88 " pdb=" OE1 GLU f 91 " model vdw 2.155 3.040 nonbonded pdb=" O ASN e 121 " pdb=" ND2 ASN e 121 " model vdw 2.166 3.120 nonbonded pdb=" OD1 ASP e 126 " pdb=" OG SER e 129 " model vdw 2.186 3.040 nonbonded pdb=" O GLN e 92 " pdb=" OH TYR e 96 " model vdw 2.204 3.040 ... (remaining 34659 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'a' and resid 27 through 54) selection = (chain 'b' and resid 27 through 54) } ncs_group { reference = (chain 'e' and (resid 33 through 69 or resid 74 through 153)) selection = (chain 'f' and resid 33 through 153) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.060 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6569 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4743 Z= 0.201 Angle : 0.710 8.769 6430 Z= 0.363 Chirality : 0.041 0.237 759 Planarity : 0.004 0.038 786 Dihedral : 17.421 88.742 1776 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 1.16 % Allowed : 36.87 % Favored : 61.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.34), residues: 569 helix: 1.39 (0.35), residues: 215 sheet: -2.08 (0.55), residues: 84 loop : -2.88 (0.32), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP f 59 HIS 0.004 0.001 HIS g 29 PHE 0.012 0.001 PHE n 296 TYR 0.025 0.002 TYR f 99 ARG 0.005 0.001 ARG e 101 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 190 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 47 THR cc_start: 0.8423 (m) cc_final: 0.8167 (p) REVERT: b 52 ARG cc_start: 0.6619 (tpt170) cc_final: 0.6358 (ttm170) REVERT: d 27 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8242 (mt-10) REVERT: d 43 TRP cc_start: 0.7895 (t60) cc_final: 0.7634 (t60) REVERT: e 72 ASP cc_start: 0.7079 (m-30) cc_final: 0.6803 (m-30) REVERT: e 74 ASN cc_start: 0.8062 (m-40) cc_final: 0.7771 (m110) REVERT: f 37 LYS cc_start: 0.7000 (ttpp) cc_final: 0.6564 (tptp) REVERT: f 60 GLN cc_start: 0.7220 (pm20) cc_final: 0.6861 (mt0) REVERT: f 117 ARG cc_start: 0.8050 (ttm170) cc_final: 0.7824 (ttp-110) REVERT: f 123 MET cc_start: 0.6624 (ttt) cc_final: 0.6176 (ttm) REVERT: g 71 LYS cc_start: 0.6165 (mtmt) cc_final: 0.5918 (mttt) REVERT: m 288 LYS cc_start: 0.7961 (tptt) cc_final: 0.7590 (tmtt) REVERT: n 275 GLN cc_start: 0.8373 (tm-30) cc_final: 0.7928 (tm-30) outliers start: 6 outliers final: 3 residues processed: 193 average time/residue: 0.1678 time to fit residues: 40.0557 Evaluate side-chains 177 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 174 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain g residue 110 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 0.9980 chunk 41 optimal weight: 0.0670 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 81 HIS f 61 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4743 Z= 0.210 Angle : 0.672 7.502 6430 Z= 0.338 Chirality : 0.042 0.170 759 Planarity : 0.004 0.039 786 Dihedral : 5.382 49.213 701 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 7.34 % Allowed : 29.15 % Favored : 63.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.35), residues: 569 helix: 2.09 (0.35), residues: 218 sheet: -2.12 (0.52), residues: 93 loop : -2.73 (0.33), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP f 59 HIS 0.005 0.001 HIS f 81 PHE 0.015 0.002 PHE n 296 TYR 0.028 0.002 TYR f 99 ARG 0.003 0.001 ARG e 117 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 176 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 52 ARG cc_start: 0.7072 (tpt170) cc_final: 0.6561 (ttm170) REVERT: d 22 PHE cc_start: 0.5145 (m-80) cc_final: 0.4401 (m-80) REVERT: d 79 TYR cc_start: 0.8181 (t80) cc_final: 0.7950 (t80) REVERT: e 40 ILE cc_start: 0.8545 (mt) cc_final: 0.8316 (mt) REVERT: e 72 ASP cc_start: 0.6966 (m-30) cc_final: 0.6660 (m-30) REVERT: e 74 ASN cc_start: 0.8128 (m-40) cc_final: 0.7779 (m110) REVERT: f 37 LYS cc_start: 0.7338 (OUTLIER) cc_final: 0.6894 (tptt) REVERT: f 79 GLU cc_start: 0.3360 (OUTLIER) cc_final: 0.2380 (mm-30) REVERT: f 92 GLN cc_start: 0.7019 (mt0) cc_final: 0.6760 (mt0) REVERT: f 106 GLU cc_start: 0.8641 (pm20) cc_final: 0.8349 (pm20) REVERT: g 71 LYS cc_start: 0.6291 (mtmt) cc_final: 0.5969 (mmtm) REVERT: m 288 LYS cc_start: 0.7988 (tptt) cc_final: 0.7638 (tmtt) REVERT: n 275 GLN cc_start: 0.8402 (tm-30) cc_final: 0.8049 (tm-30) outliers start: 38 outliers final: 24 residues processed: 190 average time/residue: 0.1710 time to fit residues: 40.3584 Evaluate side-chains 191 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 165 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 47 THR Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain b residue 47 THR Chi-restraints excluded: chain d residue 52 LEU Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 37 LYS Chi-restraints excluded: chain f residue 43 THR Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 79 GLU Chi-restraints excluded: chain f residue 134 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 110 LEU Chi-restraints excluded: chain m residue 266 LEU Chi-restraints excluded: chain n residue 293 VAL Chi-restraints excluded: chain n residue 300 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 40 optimal weight: 20.0000 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 81 HIS ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4743 Z= 0.222 Angle : 0.653 7.852 6430 Z= 0.331 Chirality : 0.041 0.135 759 Planarity : 0.003 0.035 786 Dihedral : 5.291 47.172 699 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 6.76 % Allowed : 33.20 % Favored : 60.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.36), residues: 569 helix: 2.28 (0.35), residues: 218 sheet: -2.04 (0.53), residues: 93 loop : -2.70 (0.34), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP d 43 HIS 0.004 0.001 HIS f 81 PHE 0.012 0.002 PHE n 296 TYR 0.023 0.002 TYR e 150 ARG 0.003 0.001 ARG e 117 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 172 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 52 ARG cc_start: 0.7268 (tpt170) cc_final: 0.6761 (ttm170) REVERT: d 22 PHE cc_start: 0.5557 (m-80) cc_final: 0.4173 (m-80) REVERT: d 79 TYR cc_start: 0.8158 (t80) cc_final: 0.7953 (t80) REVERT: d 90 TYR cc_start: 0.8163 (m-80) cc_final: 0.7931 (m-80) REVERT: d 98 GLU cc_start: 0.8173 (tt0) cc_final: 0.7586 (tm-30) REVERT: e 72 ASP cc_start: 0.7101 (m-30) cc_final: 0.6745 (m-30) REVERT: e 74 ASN cc_start: 0.8122 (m-40) cc_final: 0.7807 (m-40) REVERT: f 37 LYS cc_start: 0.7381 (ttpp) cc_final: 0.6914 (tptp) REVERT: f 92 GLN cc_start: 0.7254 (mt0) cc_final: 0.6961 (mt0) REVERT: f 104 LYS cc_start: 0.8520 (tptt) cc_final: 0.8211 (mmtm) REVERT: g 28 ASN cc_start: 0.8779 (t0) cc_final: 0.8407 (t0) REVERT: g 71 LYS cc_start: 0.6243 (mtmt) cc_final: 0.5966 (mmtm) REVERT: g 95 LYS cc_start: 0.8923 (mmtm) cc_final: 0.8684 (mmtm) REVERT: m 288 LYS cc_start: 0.7935 (tptt) cc_final: 0.7583 (tmtt) REVERT: m 289 LEU cc_start: 0.7834 (tp) cc_final: 0.7420 (tp) REVERT: n 275 GLN cc_start: 0.8365 (tm-30) cc_final: 0.7900 (tm-30) outliers start: 35 outliers final: 29 residues processed: 187 average time/residue: 0.1642 time to fit residues: 38.3478 Evaluate side-chains 193 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 164 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 47 THR Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain d residue 52 LEU Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 134 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 110 LEU Chi-restraints excluded: chain g residue 131 VAL Chi-restraints excluded: chain m residue 266 LEU Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 269 LEU Chi-restraints excluded: chain n residue 293 VAL Chi-restraints excluded: chain n residue 300 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 81 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4743 Z= 0.222 Angle : 0.653 8.051 6430 Z= 0.327 Chirality : 0.042 0.132 759 Planarity : 0.003 0.035 786 Dihedral : 5.184 44.515 699 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 9.65 % Allowed : 29.92 % Favored : 60.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.35), residues: 569 helix: 2.34 (0.34), residues: 217 sheet: -1.70 (0.58), residues: 82 loop : -2.75 (0.33), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP g 55 HIS 0.004 0.001 HIS f 81 PHE 0.011 0.001 PHE n 296 TYR 0.018 0.002 TYR e 150 ARG 0.004 0.001 ARG f 117 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 171 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 52 ARG cc_start: 0.7331 (tpt170) cc_final: 0.6725 (tpp-160) REVERT: d 22 PHE cc_start: 0.5633 (m-80) cc_final: 0.4045 (m-80) REVERT: e 72 ASP cc_start: 0.7098 (m-30) cc_final: 0.6702 (m-30) REVERT: f 37 LYS cc_start: 0.7255 (ttpp) cc_final: 0.6810 (tptt) REVERT: f 81 HIS cc_start: 0.6993 (OUTLIER) cc_final: 0.6627 (t70) REVERT: f 85 LYS cc_start: 0.8052 (tppt) cc_final: 0.7770 (mmmt) REVERT: f 92 GLN cc_start: 0.7481 (mt0) cc_final: 0.7069 (mt0) REVERT: f 117 ARG cc_start: 0.7930 (ttp-110) cc_final: 0.7716 (ttp-110) REVERT: g 28 ASN cc_start: 0.8776 (t0) cc_final: 0.8333 (p0) REVERT: g 71 LYS cc_start: 0.6267 (mtmt) cc_final: 0.5961 (mmtm) REVERT: g 95 LYS cc_start: 0.8853 (mmtm) cc_final: 0.8407 (mmtm) REVERT: m 288 LYS cc_start: 0.7996 (tptt) cc_final: 0.7658 (tmtt) REVERT: m 289 LEU cc_start: 0.7864 (tp) cc_final: 0.7460 (tp) outliers start: 50 outliers final: 35 residues processed: 195 average time/residue: 0.1529 time to fit residues: 37.7776 Evaluate side-chains 196 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 160 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 32 CYS Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 47 THR Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain b residue 47 THR Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain d residue 52 LEU Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 104 VAL Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 81 HIS Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 134 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 145 LEU Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 131 VAL Chi-restraints excluded: chain m residue 266 LEU Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 269 LEU Chi-restraints excluded: chain n residue 293 VAL Chi-restraints excluded: chain n residue 300 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 17 optimal weight: 0.0050 overall best weight: 1.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 81 HIS ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4743 Z= 0.244 Angle : 0.691 8.450 6430 Z= 0.341 Chirality : 0.042 0.140 759 Planarity : 0.003 0.034 786 Dihedral : 4.995 24.549 697 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 8.88 % Allowed : 30.31 % Favored : 60.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.35), residues: 569 helix: 2.30 (0.33), residues: 217 sheet: -1.79 (0.56), residues: 82 loop : -2.72 (0.33), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP g 55 HIS 0.005 0.001 HIS f 81 PHE 0.013 0.001 PHE n 296 TYR 0.017 0.002 TYR n 295 ARG 0.004 0.001 ARG e 117 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 167 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 52 ARG cc_start: 0.7333 (tpt170) cc_final: 0.6752 (tpp-160) REVERT: d 22 PHE cc_start: 0.5153 (m-80) cc_final: 0.4202 (m-80) REVERT: d 79 TYR cc_start: 0.7960 (t80) cc_final: 0.7740 (t80) REVERT: e 72 ASP cc_start: 0.7172 (m-30) cc_final: 0.6758 (m-30) REVERT: f 37 LYS cc_start: 0.7245 (ttpp) cc_final: 0.6772 (tptp) REVERT: f 81 HIS cc_start: 0.7016 (OUTLIER) cc_final: 0.6613 (t70) REVERT: f 85 LYS cc_start: 0.8072 (tppt) cc_final: 0.7826 (mmmt) REVERT: f 92 GLN cc_start: 0.7657 (mt0) cc_final: 0.7249 (mt0) REVERT: f 106 GLU cc_start: 0.8651 (pm20) cc_final: 0.8401 (pm20) REVERT: g 28 ASN cc_start: 0.8779 (t0) cc_final: 0.8302 (p0) REVERT: g 95 LYS cc_start: 0.8821 (mmtm) cc_final: 0.8285 (mmtm) REVERT: m 288 LYS cc_start: 0.7985 (tptt) cc_final: 0.7655 (tmtt) REVERT: m 289 LEU cc_start: 0.7979 (tp) cc_final: 0.7551 (tp) outliers start: 46 outliers final: 40 residues processed: 187 average time/residue: 0.1642 time to fit residues: 38.9681 Evaluate side-chains 201 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 160 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 32 CYS Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 47 THR Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain b residue 47 THR Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain d residue 52 LEU Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 104 VAL Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 41 SER Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 81 HIS Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 134 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 110 LEU Chi-restraints excluded: chain g residue 124 VAL Chi-restraints excluded: chain g residue 131 VAL Chi-restraints excluded: chain m residue 266 LEU Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 269 LEU Chi-restraints excluded: chain n residue 293 VAL Chi-restraints excluded: chain n residue 300 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 24 optimal weight: 0.0980 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4743 Z= 0.191 Angle : 0.666 9.211 6430 Z= 0.325 Chirality : 0.042 0.171 759 Planarity : 0.003 0.033 786 Dihedral : 4.796 26.073 697 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 8.30 % Allowed : 32.24 % Favored : 59.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.35), residues: 569 helix: 2.42 (0.34), residues: 217 sheet: -1.99 (0.53), residues: 92 loop : -2.59 (0.34), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP g 55 HIS 0.005 0.001 HIS f 81 PHE 0.019 0.001 PHE e 110 TYR 0.014 0.001 TYR e 150 ARG 0.004 0.000 ARG e 117 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 168 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 22 PHE cc_start: 0.4947 (m-80) cc_final: 0.3853 (m-80) REVERT: e 72 ASP cc_start: 0.7197 (m-30) cc_final: 0.6806 (m-30) REVERT: f 37 LYS cc_start: 0.7241 (ttpp) cc_final: 0.6825 (tptp) REVERT: f 81 HIS cc_start: 0.6987 (OUTLIER) cc_final: 0.6673 (t70) REVERT: f 85 LYS cc_start: 0.8117 (tppt) cc_final: 0.7835 (mmmt) REVERT: f 92 GLN cc_start: 0.7694 (mt0) cc_final: 0.7258 (mt0) REVERT: f 106 GLU cc_start: 0.8590 (pm20) cc_final: 0.8333 (pm20) REVERT: g 28 ASN cc_start: 0.8766 (t0) cc_final: 0.8180 (p0) REVERT: g 85 TYR cc_start: 0.8138 (m-80) cc_final: 0.7796 (m-80) REVERT: g 95 LYS cc_start: 0.8832 (mmtm) cc_final: 0.8274 (mmtm) REVERT: m 289 LEU cc_start: 0.7927 (tp) cc_final: 0.7499 (tp) outliers start: 43 outliers final: 37 residues processed: 188 average time/residue: 0.1501 time to fit residues: 35.9959 Evaluate side-chains 201 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 163 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 32 CYS Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 47 THR Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain b residue 55 PHE Chi-restraints excluded: chain d residue 52 LEU Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 43 THR Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 81 HIS Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 134 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 145 LEU Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 110 LEU Chi-restraints excluded: chain g residue 124 VAL Chi-restraints excluded: chain m residue 266 LEU Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain n residue 300 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 0.0040 chunk 30 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4743 Z= 0.248 Angle : 0.735 9.217 6430 Z= 0.356 Chirality : 0.042 0.134 759 Planarity : 0.003 0.034 786 Dihedral : 5.060 29.523 697 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 9.27 % Allowed : 30.89 % Favored : 59.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.35), residues: 569 helix: 2.38 (0.34), residues: 216 sheet: -1.97 (0.56), residues: 87 loop : -2.57 (0.34), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP g 55 HIS 0.005 0.001 HIS f 81 PHE 0.014 0.002 PHE e 110 TYR 0.019 0.002 TYR n 295 ARG 0.014 0.001 ARG b 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 172 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 52 ARG cc_start: 0.7959 (ttp80) cc_final: 0.6556 (tpp-160) REVERT: e 72 ASP cc_start: 0.7314 (m-30) cc_final: 0.6894 (m-30) REVERT: e 109 ASN cc_start: 0.7626 (m-40) cc_final: 0.7127 (p0) REVERT: f 37 LYS cc_start: 0.7336 (ttpp) cc_final: 0.6984 (tptp) REVERT: f 81 HIS cc_start: 0.7075 (OUTLIER) cc_final: 0.6755 (t70) REVERT: f 92 GLN cc_start: 0.7759 (mt0) cc_final: 0.7350 (mt0) REVERT: g 28 ASN cc_start: 0.8771 (t0) cc_final: 0.8290 (t0) REVERT: g 95 LYS cc_start: 0.8842 (mmtm) cc_final: 0.8589 (mmtm) REVERT: m 289 LEU cc_start: 0.7934 (tp) cc_final: 0.7494 (tp) outliers start: 48 outliers final: 42 residues processed: 197 average time/residue: 0.1488 time to fit residues: 37.0934 Evaluate side-chains 209 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 166 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 32 CYS Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain b residue 32 CYS Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 47 THR Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain d residue 52 LEU Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 104 VAL Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 86 GLU Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 43 THR Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 81 HIS Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 133 ILE Chi-restraints excluded: chain f residue 134 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 145 LEU Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 124 VAL Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 269 LEU Chi-restraints excluded: chain n residue 293 VAL Chi-restraints excluded: chain n residue 300 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 36 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4743 Z= 0.202 Angle : 0.748 9.741 6430 Z= 0.361 Chirality : 0.042 0.152 759 Planarity : 0.003 0.032 786 Dihedral : 4.983 27.324 697 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 7.53 % Allowed : 33.98 % Favored : 58.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.35), residues: 569 helix: 2.50 (0.34), residues: 215 sheet: -1.83 (0.54), residues: 92 loop : -2.62 (0.33), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP g 55 HIS 0.005 0.001 HIS f 81 PHE 0.008 0.001 PHE n 296 TYR 0.018 0.002 TYR n 283 ARG 0.008 0.001 ARG b 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 170 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 52 ARG cc_start: 0.7902 (ttp80) cc_final: 0.6466 (ttm170) REVERT: d 22 PHE cc_start: 0.4543 (m-80) cc_final: 0.3833 (m-80) REVERT: d 43 TRP cc_start: 0.7088 (t60) cc_final: 0.6696 (t60) REVERT: d 79 TYR cc_start: 0.8222 (t80) cc_final: 0.7946 (t80) REVERT: e 72 ASP cc_start: 0.7294 (m-30) cc_final: 0.6896 (m-30) REVERT: e 91 GLU cc_start: 0.7795 (tp30) cc_final: 0.7413 (tp30) REVERT: e 92 GLN cc_start: 0.7889 (pm20) cc_final: 0.7683 (pm20) REVERT: e 109 ASN cc_start: 0.7657 (m-40) cc_final: 0.7121 (p0) REVERT: e 125 MET cc_start: 0.7059 (pmm) cc_final: 0.6857 (pmm) REVERT: f 37 LYS cc_start: 0.7351 (ttpp) cc_final: 0.7026 (tptp) REVERT: f 92 GLN cc_start: 0.7670 (mt0) cc_final: 0.7312 (mt0) REVERT: g 28 ASN cc_start: 0.8782 (t0) cc_final: 0.8303 (p0) REVERT: g 85 TYR cc_start: 0.8097 (m-80) cc_final: 0.7770 (m-80) REVERT: g 95 LYS cc_start: 0.8773 (mmtm) cc_final: 0.8167 (mmtm) REVERT: m 289 LEU cc_start: 0.7985 (tp) cc_final: 0.7534 (tp) outliers start: 39 outliers final: 34 residues processed: 189 average time/residue: 0.1507 time to fit residues: 36.1958 Evaluate side-chains 200 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 166 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 42 TYR Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain b residue 32 CYS Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain d residue 52 LEU Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 86 GLU Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 43 THR Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 134 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 145 LEU Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 124 VAL Chi-restraints excluded: chain m residue 266 LEU Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 269 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 32 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4743 Z= 0.217 Angle : 0.761 9.066 6430 Z= 0.366 Chirality : 0.042 0.170 759 Planarity : 0.003 0.032 786 Dihedral : 4.993 26.878 697 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 6.56 % Allowed : 34.94 % Favored : 58.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.36), residues: 569 helix: 2.44 (0.34), residues: 217 sheet: -1.78 (0.51), residues: 97 loop : -2.56 (0.34), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP g 55 HIS 0.005 0.001 HIS f 81 PHE 0.016 0.001 PHE n 296 TYR 0.025 0.002 TYR n 283 ARG 0.008 0.001 ARG b 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 171 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 22 PHE cc_start: 0.4457 (m-80) cc_final: 0.3658 (m-80) REVERT: d 43 TRP cc_start: 0.7111 (t60) cc_final: 0.6729 (t60) REVERT: d 79 TYR cc_start: 0.8189 (t80) cc_final: 0.7894 (t80) REVERT: e 72 ASP cc_start: 0.7308 (m-30) cc_final: 0.6915 (m-30) REVERT: e 91 GLU cc_start: 0.7722 (tp30) cc_final: 0.7453 (tp30) REVERT: e 109 ASN cc_start: 0.7649 (m-40) cc_final: 0.7125 (p0) REVERT: f 37 LYS cc_start: 0.7383 (ttpp) cc_final: 0.7039 (tptp) REVERT: f 92 GLN cc_start: 0.7701 (mt0) cc_final: 0.7341 (mt0) REVERT: m 264 MET cc_start: 0.7571 (tpp) cc_final: 0.7337 (tpp) outliers start: 34 outliers final: 31 residues processed: 186 average time/residue: 0.1554 time to fit residues: 36.4758 Evaluate side-chains 197 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 166 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain b residue 32 CYS Chi-restraints excluded: chain b residue 36 ASP Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain d residue 52 LEU Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 43 THR Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 134 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 145 LEU Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 110 LEU Chi-restraints excluded: chain g residue 124 VAL Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 269 LEU Chi-restraints excluded: chain n residue 293 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 0.0870 chunk 36 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 28 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6607 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4743 Z= 0.213 Angle : 0.781 8.823 6430 Z= 0.372 Chirality : 0.042 0.198 759 Planarity : 0.003 0.032 786 Dihedral : 4.957 26.439 697 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 6.37 % Allowed : 36.29 % Favored : 57.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.35), residues: 569 helix: 2.41 (0.34), residues: 217 sheet: -1.69 (0.53), residues: 92 loop : -2.58 (0.33), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP g 55 HIS 0.005 0.001 HIS f 81 PHE 0.018 0.001 PHE n 296 TYR 0.020 0.001 TYR n 283 ARG 0.002 0.000 ARG e 117 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 170 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 52 ARG cc_start: 0.7850 (tmm-80) cc_final: 0.6607 (ttm170) REVERT: d 22 PHE cc_start: 0.4534 (m-80) cc_final: 0.3701 (m-80) REVERT: d 43 TRP cc_start: 0.7061 (t60) cc_final: 0.6690 (t60) REVERT: d 79 TYR cc_start: 0.8185 (t80) cc_final: 0.7873 (t80) REVERT: e 109 ASN cc_start: 0.7692 (m-40) cc_final: 0.7183 (p0) REVERT: f 37 LYS cc_start: 0.7542 (ttpp) cc_final: 0.7274 (tptp) REVERT: f 92 GLN cc_start: 0.7674 (mt0) cc_final: 0.7338 (mt0) REVERT: g 28 ASN cc_start: 0.8711 (t0) cc_final: 0.8340 (p0) REVERT: g 85 TYR cc_start: 0.8162 (m-80) cc_final: 0.7855 (m-80) REVERT: m 264 MET cc_start: 0.7518 (tpp) cc_final: 0.7278 (tpp) REVERT: m 289 LEU cc_start: 0.7956 (tp) cc_final: 0.7722 (tp) REVERT: n 275 GLN cc_start: 0.8349 (tm-30) cc_final: 0.7826 (tt0) outliers start: 33 outliers final: 30 residues processed: 185 average time/residue: 0.1529 time to fit residues: 36.0500 Evaluate side-chains 197 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 167 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain b residue 32 CYS Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain d residue 52 LEU Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain e residue 39 SER Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 97 VAL Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 43 THR Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 134 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 145 LEU Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain f residue 148 VAL Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 124 VAL Chi-restraints excluded: chain m residue 266 LEU Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 269 LEU Chi-restraints excluded: chain n residue 300 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 8 optimal weight: 0.0470 chunk 38 optimal weight: 1.9990 chunk 2 optimal weight: 0.1980 chunk 31 optimal weight: 6.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.160182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.131703 restraints weight = 7459.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.135921 restraints weight = 4066.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.138832 restraints weight = 2758.721| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4743 Z= 0.214 Angle : 0.781 8.958 6430 Z= 0.371 Chirality : 0.042 0.200 759 Planarity : 0.003 0.031 786 Dihedral : 4.945 26.716 697 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 6.76 % Allowed : 35.52 % Favored : 57.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.35), residues: 569 helix: 2.39 (0.34), residues: 218 sheet: -1.55 (0.53), residues: 92 loop : -2.60 (0.34), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP d 43 HIS 0.005 0.001 HIS f 81 PHE 0.018 0.001 PHE n 296 TYR 0.019 0.001 TYR n 283 ARG 0.002 0.000 ARG e 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1405.05 seconds wall clock time: 25 minutes 36.47 seconds (1536.47 seconds total)